Esempio n. 1
0
void RunQSNP::run()
{
    Configuration* pConfig = Configuration::getConfig();

    Logger* pLogger = Logger::getLogger();
    pLogger->log(QSNP_ALWAYS, "QualitySNP started with settings: " + pConfig->toString());

    ContigProvider contigProvider;
    if (!contigProvider.init()) {
        emit reportError("Could read contig file");
        return;
    }

    vector<string> readGroups;
    if(pConfig->getBool("outputReadGroups")) {
        readGroups = contigProvider.getReadGroups();
    }

    CSVWriter csvWriter(readGroups);
    if (!csvWriter.init()) {
        emit reportError("Could not write results");
        emit done();
        return;
    }

    pConfig->writeFile("config.cfg", pConfig->getString("outputDirectory"));

    QString message;

    if(pConfig->getBool("collectStatistics")) {
        message = QString("Processing a total of %1 contigs with %2 reads").arg(contigProvider.getContigCount()).arg(contigProvider.getReadCount());
        emit printMessage(message);
    }

    QMutex mutex;
    Contig* pContig = contigProvider.nextContig();
    while (pContig != NULL && !_bCancelled) {
        message = "Processing: " + QString::fromStdString(pContig->getName());
        emit printMessage(message);

        QSNPRunTask *runTask = new QSNPRunTask();
        runTask->setContig(pContig);
        runTask->setWriter(&csvWriter);
        runTask->setShowContigsWithoutSNP(pConfig->getBool("showContigsWithoutSNP"));
        runTask->setMutex(&mutex);

        while(!QThreadPool::globalInstance()->tryStart(runTask)) {
            I::msleep(1); // sleep for 1 millisecond before trying again
        }

        message = "Done";
        emit printMessage(message);

        pContig = contigProvider.nextContig();
    }

    QThreadPool::globalInstance()->waitForDone();

    emit done();
}
Esempio n. 2
0
int KEduVocDocument::saveAs( const KUrl & url, FileType ft, const QString & generator )
{
    KUrl tmp( url );

    if ( ft == Automatic ) {
        if ( tmp.path().right( strlen( "." KVTML_EXT ) ) == "." KVTML_EXT )
            ft = Kvtml;
        else if ( tmp.path().right( strlen( "." CSV_EXT ) ) == "." CSV_EXT )
            ft = Csv;
        else {
            return FileTypeUnknown;
        }
    }

    QFile f( tmp.path() );

    if ( !f.open( QIODevice::WriteOnly ) ) {
        kError() << i18n( "Cannot write to file %1", tmp.path() );
        return FileCannotWrite;
    }

    KUrl oldUrl = d->m_url;
    bool saved = false;
    d->m_url = tmp;

    switch ( ft ) {
        case Kvtml: {
            // write version 2 file
            KEduVocKvtml2Writer kvtmlWriter( &f );
            saved = kvtmlWriter.writeDoc( this, generator );
        }
        break;
        ///@todo port me
//         case Kvtml1: {
//             // write old version 1 file
//             KEduVocKvtmlWriter kvtmlWriter( &f );
//             saved = kvtmlWriter.writeDoc( this, generator );
//         }
//         break;
        case Csv: {
            KEduVocCsvWriter csvWriter( &f );
            saved = csvWriter.writeDoc( this, generator );
        }
        break;
        default: {
            kError() << "kvcotrainDoc::saveAs(): unknown filetype" << endl;
        }
        break;
    } // switch

    f.close();

    if ( !saved ) {
        kError() << "Error Saving File" << tmp.path();
        d->m_url = oldUrl;
        return FileWriterFailed;
    }

    setModified( false );
    return 0;
}